Emergence of decapod hepanhamaparvovirus genotype V and its co-infection with Enterocytozoon hepatopenaei in cultured Penaeus vannamei in Thailand: Evidence from epidemiological, pathogenicity, and microbiome analyses.

Background and Aim: Growth retardation syndrome in cultured Penaeus vannamei has been associated with Enterocytozoon hepatopenaei (EHP) and a recently identified decapod hepanhamaparvovirus (DHPV) genotype V. However, data on its prevalence, pathogenicity, and interaction with the shrimp hepatopancreatic microbiome in Thailand remain limited. This study aimed to determine the incidence and co-infection rate of DHPV genotype V with EHP, evaluate its pathogenic potential, and explore microbiome alterations associated with infection. Materials and Methods: Between 2022 and 2023, 1,270 shrimp from 127 grow-out ponds across 46 farms in eastern Thailand and post-larvae 12 from five hatcheries in the south were screened for DHPV and EHP by polymerase chain reaction. Six representative isolates underwent phylogenetic analysis based on non-structural protein 1 (NS1) and NS2 genes. Pathogenicity was evaluated by immersion challenge bioassays in specific pathogen-free P. vannamei. Hepatopancreatic microbiomes of naturally infected and healthy shrimp were compared using 16S ribosomal RNA gene sequencing and Quantitative Insights Into Microbial Ecology 2-based analysis. Results: DHPV was detected in 54.33% (69/127) of ponds and 4% (1/25) of hatchery tanks. Co-infection with EHP occurred in 40.16% of ponds. Phylogenetic analysis showed 97.99%-98.82% similarity with DHPV genotype V from South Korea, confirming transboundary genetic relatedness. Experimental infection caused low mortality (20%) but resulted in viral replication (101-103 copies/μL) and characteristic intranuclear inclusion bodies in hepatopancreatic cells. DHPV-infected shrimp exhibited distinct microbiome profiles with elevated Firmicutes, Planctomycetota, and Actinobacteriota abundances, supporting a pathobiome shift during infection. Conclusion: This is the first report of DHPV genotype V in P. vannamei from Thailand and its frequent co-infection with EHP. Despite its low experimental virulence, the widespread occurrence and microbiome dysbiosis suggest that it may have subclinical impacts that could exacerbate growth retardation. Routine molecular screening in hatcheries and farms, coupled with integrated viral-microbiome surveillance, is essential for sustainable aquaculture biosecurity and aligns with the United Nations Sustainable Development Goal 14 (Life Below Water) by promoting resilient aquatic food systems.